Starting phenix.real_space_refine on Tue Feb 3 17:01:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lou_63260/02_2026/9lou_63260.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lou_63260/02_2026/9lou_63260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lou_63260/02_2026/9lou_63260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lou_63260/02_2026/9lou_63260.map" model { file = "/net/cci-nas-00/data/ceres_data/9lou_63260/02_2026/9lou_63260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lou_63260/02_2026/9lou_63260.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 28 5.49 5 Mg 1 5.21 5 S 28 5.16 5 C 3212 2.51 5 N 965 2.21 5 O 1045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5280 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4732 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 574} Chain breaks: 4 Chain: "X" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 269 Unusual residues: {'GTP': 1} Classifications: {'RNA': 11, 'undetermined': 1} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 4} Link IDs: {'rna3p': 10, None: 1} Not linked: pdbres="GTP X 1 " pdbres=" A X 2 " Chain: "Y" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3806 SG CYS A 556 61.626 23.071 57.700 1.00 76.86 S ATOM 3828 SG CYS A 559 63.139 20.116 60.401 1.00 82.01 S ATOM 4267 SG CYS A 615 59.977 20.342 58.642 1.00 82.08 S Time building chain proxies: 1.29, per 1000 atoms: 0.24 Number of scatterers: 5280 At special positions: 0 Unit cell: (88.81, 87.98, 89.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 28 16.00 P 28 15.00 Mg 1 11.99 O 1045 8.00 N 965 7.00 C 3212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 377.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 615 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 559 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 556 " 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 55.0% alpha, 11.7% beta 9 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 removed outlier: 3.893A pdb=" N GLU A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 11 " --> pdb=" O GLN A 7 " (cutoff:3.500A) Proline residue: A 13 - end of helix removed outlier: 4.003A pdb=" N GLU A 16 " --> pdb=" O MET A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 56 through 71 removed outlier: 3.804A pdb=" N VAL A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 62 " --> pdb=" O HIS A 58 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.521A pdb=" N PHE A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 136 Processing helix chain 'A' and resid 140 through 156 removed outlier: 3.607A pdb=" N GLN A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.580A pdb=" N GLU A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 273 Processing helix chain 'A' and resid 274 through 297 removed outlier: 3.553A pdb=" N ARG A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.658A pdb=" N ALA A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS A 314 " --> pdb=" O TYR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 345 removed outlier: 3.503A pdb=" N ASP A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN A 336 " --> pdb=" O ASP A 332 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N HIS A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 362 Processing helix chain 'A' and resid 377 through 390 removed outlier: 3.618A pdb=" N GLN A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 removed outlier: 3.573A pdb=" N THR A 395 " --> pdb=" O GLN A 391 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 removed outlier: 3.525A pdb=" N GLU A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 514 through 544 removed outlier: 3.532A pdb=" N ALA A 520 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 551 Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.805A pdb=" N VAL A 655 " --> pdb=" O TRP A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 672 removed outlier: 3.522A pdb=" N GLU A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.447A pdb=" N THR A 78 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR A 103 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL A 50 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N CYS A 102 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL A 52 " --> pdb=" O CYS A 102 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 21 " --> pdb=" O CYS A 196 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP A 23 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 434 through 437 removed outlier: 6.991A pdb=" N GLY A 370 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA A 437 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE A 372 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 454 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 562 through 565 Processing sheet with id=AA4, first strand: chain 'A' and resid 569 through 572 removed outlier: 3.528A pdb=" N VAL A 578 " --> pdb=" O ARG A 570 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 588 through 590 removed outlier: 5.276A pdb=" N GLN A 622 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL A 609 " --> pdb=" O GLY A 620 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY A 620 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER A 611 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 618 " --> pdb=" O SER A 611 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 684 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1495 1.33 - 1.45: 929 1.45 - 1.57: 2904 1.57 - 1.69: 52 1.69 - 1.81: 44 Bond restraints: 5424 Sorted by residual: bond pdb=" C4 ADP A 701 " pdb=" C5 ADP A 701 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" C LEU A 402 " pdb=" N LEU A 403 " ideal model delta sigma weight residual 1.333 1.345 -0.012 1.30e-02 5.92e+03 8.02e-01 bond pdb=" C2' GTP X 1 " pdb=" C3' GTP X 1 " ideal model delta sigma weight residual 1.524 1.510 0.014 2.00e-02 2.50e+03 4.58e-01 bond pdb=" CA SER A 367 " pdb=" C SER A 367 " ideal model delta sigma weight residual 1.524 1.532 -0.008 1.26e-02 6.30e+03 4.02e-01 bond pdb=" CA SER A 199 " pdb=" C SER A 199 " ideal model delta sigma weight residual 1.519 1.525 -0.006 1.01e-02 9.80e+03 3.34e-01 ... (remaining 5419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 7393 1.79 - 3.59: 50 3.59 - 5.38: 10 5.38 - 7.18: 3 7.18 - 8.97: 1 Bond angle restraints: 7457 Sorted by residual: angle pdb=" C2' GTP X 1 " pdb=" C3' GTP X 1 " pdb=" C4' GTP X 1 " ideal model delta sigma weight residual 111.00 102.03 8.97 3.00e+00 1.11e-01 8.94e+00 angle pdb=" CA GLY A 171 " pdb=" C GLY A 171 " pdb=" O GLY A 171 " ideal model delta sigma weight residual 122.24 120.58 1.66 8.70e-01 1.32e+00 3.64e+00 angle pdb=" C1' GTP X 1 " pdb=" C2' GTP X 1 " pdb=" C3' GTP X 1 " ideal model delta sigma weight residual 111.00 105.33 5.67 3.00e+00 1.11e-01 3.57e+00 angle pdb=" O1B ADP A 701 " pdb=" PB ADP A 701 " pdb=" O2B ADP A 701 " ideal model delta sigma weight residual 119.90 114.25 5.65 3.00e+00 1.11e-01 3.54e+00 angle pdb=" O1B ADP A 701 " pdb=" PB ADP A 701 " pdb=" O3B ADP A 701 " ideal model delta sigma weight residual 119.90 114.45 5.45 3.00e+00 1.11e-01 3.30e+00 ... (remaining 7452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.37: 2994 18.37 - 36.74: 221 36.74 - 55.11: 49 55.11 - 73.48: 29 73.48 - 91.85: 7 Dihedral angle restraints: 3300 sinusoidal: 1570 harmonic: 1730 Sorted by residual: dihedral pdb=" C8 GTP X 1 " pdb=" C1' GTP X 1 " pdb=" N9 GTP X 1 " pdb=" O4' GTP X 1 " ideal model delta sinusoidal sigma weight residual 104.59 12.74 91.85 1 2.00e+01 2.50e-03 2.48e+01 dihedral pdb=" C4' GTP X 1 " pdb=" C5' GTP X 1 " pdb=" O5' GTP X 1 " pdb=" PA GTP X 1 " ideal model delta sinusoidal sigma weight residual 260.87 174.24 86.63 1 2.00e+01 2.50e-03 2.26e+01 dihedral pdb=" CA ARG A 369 " pdb=" CB ARG A 369 " pdb=" CG ARG A 369 " pdb=" CD ARG A 369 " ideal model delta sinusoidal sigma weight residual -60.00 -117.88 57.88 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 645 0.033 - 0.066: 149 0.066 - 0.099: 44 0.099 - 0.132: 22 0.132 - 0.165: 2 Chirality restraints: 862 Sorted by residual: chirality pdb=" C2' GTP X 1 " pdb=" C1' GTP X 1 " pdb=" C3' GTP X 1 " pdb=" O2' GTP X 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.64 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA VAL A 120 " pdb=" N VAL A 120 " pdb=" C VAL A 120 " pdb=" CB VAL A 120 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE A 197 " pdb=" N ILE A 197 " pdb=" C ILE A 197 " pdb=" CB ILE A 197 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 859 not shown) Planarity restraints: 870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 348 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 349 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 349 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 349 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 642 " -0.016 5.00e-02 4.00e+02 2.46e-02 9.70e-01 pdb=" N PRO A 643 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 643 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 643 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 12 " 0.014 5.00e-02 4.00e+02 2.10e-02 7.09e-01 pdb=" N PRO A 13 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO A 13 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 13 " 0.012 5.00e-02 4.00e+02 ... (remaining 867 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 3 2.15 - 2.84: 1631 2.84 - 3.53: 7355 3.53 - 4.21: 12781 4.21 - 4.90: 21308 Nonbonded interactions: 43078 Sorted by model distance: nonbonded pdb=" O3' GTP X 1 " pdb=" OP1 A X 2 " model vdw 1.465 3.040 nonbonded pdb=" O3' GTP X 1 " pdb=" P A X 2 " model vdw 1.722 3.400 nonbonded pdb=" C3' GTP X 1 " pdb=" P A X 2 " model vdw 2.078 3.830 nonbonded pdb=" OH TYR A 6 " pdb=" O ALA A 28 " model vdw 2.223 3.040 nonbonded pdb=" O THR A 296 " pdb=" OH TYR A 456 " model vdw 2.226 3.040 ... (remaining 43073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.400 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5427 Z= 0.093 Angle : 0.450 8.972 7457 Z= 0.222 Chirality : 0.036 0.165 862 Planarity : 0.003 0.030 870 Dihedral : 15.046 91.850 2174 Min Nonbonded Distance : 1.465 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.78 % Allowed : 9.71 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.35), residues: 586 helix: 1.03 (0.31), residues: 265 sheet: -0.80 (0.58), residues: 90 loop : 0.08 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 298 TYR 0.007 0.001 TYR A 588 PHE 0.006 0.001 PHE A 584 TRP 0.006 0.001 TRP A 75 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 5424) covalent geometry : angle 0.44967 ( 7457) hydrogen bonds : bond 0.29705 ( 261) hydrogen bonds : angle 8.15580 ( 726) metal coordination : bond 0.00145 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8360 (m-30) cc_final: 0.7936 (t0) REVERT: A 264 LYS cc_start: 0.6643 (mptt) cc_final: 0.6006 (ttmt) REVERT: A 287 TYR cc_start: 0.8241 (m-80) cc_final: 0.8001 (m-80) REVERT: A 311 HIS cc_start: 0.6548 (m-70) cc_final: 0.6255 (m90) REVERT: A 321 LEU cc_start: 0.6902 (mt) cc_final: 0.6681 (mp) REVERT: A 347 GLU cc_start: 0.6714 (pm20) cc_final: 0.5028 (tt0) REVERT: A 378 GLN cc_start: 0.6985 (mt0) cc_final: 0.6581 (mp10) REVERT: A 604 TRP cc_start: 0.8115 (p-90) cc_final: 0.7838 (p-90) REVERT: A 626 LYS cc_start: 0.7271 (mttt) cc_final: 0.7025 (ttmt) outliers start: 4 outliers final: 1 residues processed: 142 average time/residue: 0.1065 time to fit residues: 18.4971 Evaluate side-chains 76 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 63 HIS A 119 HIS A 359 GLN A 414 HIS A 505 GLN A 515 GLN A 519 GLN A 666 GLN ** A 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.170976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.143964 restraints weight = 6741.800| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.31 r_work: 0.3630 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5427 Z= 0.139 Angle : 0.588 7.605 7457 Z= 0.290 Chirality : 0.041 0.172 862 Planarity : 0.004 0.029 870 Dihedral : 13.417 87.056 1017 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.33 % Allowed : 13.20 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.34), residues: 586 helix: 1.75 (0.30), residues: 274 sheet: -1.12 (0.52), residues: 104 loop : -0.34 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 425 TYR 0.020 0.002 TYR A 258 PHE 0.019 0.002 PHE A 664 TRP 0.010 0.001 TRP A 652 HIS 0.006 0.001 HIS A 667 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5424) covalent geometry : angle 0.58848 ( 7457) hydrogen bonds : bond 0.04762 ( 261) hydrogen bonds : angle 4.72794 ( 726) metal coordination : bond 0.00098 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8481 (m-30) cc_final: 0.7868 (t0) REVERT: A 179 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7223 (m-30) REVERT: A 238 ASP cc_start: 0.6821 (m-30) cc_final: 0.6613 (m-30) REVERT: A 255 THR cc_start: 0.8062 (m) cc_final: 0.7641 (p) REVERT: A 264 LYS cc_start: 0.6560 (mptt) cc_final: 0.6030 (ttmt) REVERT: A 303 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7142 (tp) REVERT: A 347 GLU cc_start: 0.6803 (pm20) cc_final: 0.5467 (tt0) REVERT: A 353 MET cc_start: 0.7915 (ttm) cc_final: 0.7044 (mmt) outliers start: 12 outliers final: 3 residues processed: 99 average time/residue: 0.0653 time to fit residues: 8.8966 Evaluate side-chains 81 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 627 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 201 GLN A 260 GLN A 314 HIS A 394 GLN A 511 GLN A 576 HIS ** A 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.169930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.143914 restraints weight = 6908.067| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.22 r_work: 0.3646 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5427 Z= 0.132 Angle : 0.549 7.230 7457 Z= 0.269 Chirality : 0.040 0.156 862 Planarity : 0.003 0.027 870 Dihedral : 13.435 85.113 1016 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.11 % Allowed : 15.15 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.34), residues: 586 helix: 2.08 (0.30), residues: 274 sheet: -1.19 (0.59), residues: 80 loop : -0.38 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 285 TYR 0.021 0.002 TYR A 518 PHE 0.009 0.001 PHE A 309 TRP 0.009 0.001 TRP A 386 HIS 0.004 0.001 HIS A 667 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5424) covalent geometry : angle 0.54934 ( 7457) hydrogen bonds : bond 0.04205 ( 261) hydrogen bonds : angle 4.47066 ( 726) metal coordination : bond 0.00119 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8465 (m-30) cc_final: 0.7922 (t0) REVERT: A 248 GLU cc_start: 0.7339 (pm20) cc_final: 0.7115 (pm20) REVERT: A 264 LYS cc_start: 0.6586 (mptt) cc_final: 0.6088 (ttmt) REVERT: A 353 MET cc_start: 0.7814 (ttm) cc_final: 0.7118 (mmt) REVERT: A 455 ARG cc_start: 0.6758 (mmm-85) cc_final: 0.6287 (ptt-90) outliers start: 16 outliers final: 7 residues processed: 90 average time/residue: 0.0775 time to fit residues: 9.3232 Evaluate side-chains 73 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 627 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.168505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.142565 restraints weight = 6810.078| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.18 r_work: 0.3647 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5427 Z= 0.130 Angle : 0.534 7.360 7457 Z= 0.260 Chirality : 0.040 0.153 862 Planarity : 0.003 0.027 870 Dihedral : 13.530 83.245 1016 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.14 % Allowed : 16.89 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.34), residues: 586 helix: 2.07 (0.29), residues: 280 sheet: -1.32 (0.58), residues: 80 loop : -0.32 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.022 0.002 TYR A 588 PHE 0.009 0.001 PHE A 309 TRP 0.009 0.001 TRP A 604 HIS 0.005 0.001 HIS A 667 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 5424) covalent geometry : angle 0.53370 ( 7457) hydrogen bonds : bond 0.03785 ( 261) hydrogen bonds : angle 4.30916 ( 726) metal coordination : bond 0.00119 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8452 (m-30) cc_final: 0.7887 (t0) REVERT: A 248 GLU cc_start: 0.7422 (pm20) cc_final: 0.7220 (pm20) REVERT: A 264 LYS cc_start: 0.6612 (mptt) cc_final: 0.6125 (ttmt) REVERT: A 271 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7957 (mp) REVERT: A 347 GLU cc_start: 0.6823 (pm20) cc_final: 0.5930 (tt0) REVERT: A 353 MET cc_start: 0.7948 (ttm) cc_final: 0.7087 (mmt) REVERT: A 455 ARG cc_start: 0.6809 (mmm-85) cc_final: 0.6289 (ptt-90) REVERT: A 626 LYS cc_start: 0.7386 (ttpt) cc_final: 0.6934 (ptmt) outliers start: 11 outliers final: 7 residues processed: 83 average time/residue: 0.0769 time to fit residues: 8.5687 Evaluate side-chains 77 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 609 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 0.0470 chunk 58 optimal weight: 0.0060 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 0.0010 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 0.0970 overall best weight: 0.0698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.177008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.151562 restraints weight = 7049.341| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.23 r_work: 0.3738 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5427 Z= 0.087 Angle : 0.495 7.366 7457 Z= 0.238 Chirality : 0.037 0.135 862 Planarity : 0.003 0.025 870 Dihedral : 13.612 82.474 1016 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.55 % Allowed : 17.86 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.35), residues: 586 helix: 2.36 (0.30), residues: 284 sheet: -1.29 (0.52), residues: 99 loop : -0.22 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 285 TYR 0.024 0.002 TYR A 518 PHE 0.010 0.001 PHE A 362 TRP 0.010 0.001 TRP A 386 HIS 0.007 0.001 HIS A 381 Details of bonding type rmsd covalent geometry : bond 0.00172 ( 5424) covalent geometry : angle 0.49504 ( 7457) hydrogen bonds : bond 0.03136 ( 261) hydrogen bonds : angle 4.01477 ( 726) metal coordination : bond 0.00020 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8385 (m-30) cc_final: 0.7841 (t0) REVERT: A 264 LYS cc_start: 0.6551 (mptt) cc_final: 0.6073 (ttmt) REVERT: A 347 GLU cc_start: 0.6755 (pm20) cc_final: 0.5940 (tt0) REVERT: A 353 MET cc_start: 0.7903 (ttm) cc_final: 0.7075 (mmt) REVERT: A 626 LYS cc_start: 0.7284 (ttpt) cc_final: 0.6717 (ptpt) outliers start: 8 outliers final: 6 residues processed: 85 average time/residue: 0.0865 time to fit residues: 9.7503 Evaluate side-chains 77 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.166838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.140999 restraints weight = 6925.282| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.17 r_work: 0.3648 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5427 Z= 0.164 Angle : 0.566 7.762 7457 Z= 0.273 Chirality : 0.041 0.184 862 Planarity : 0.003 0.027 870 Dihedral : 13.610 83.032 1016 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.72 % Allowed : 17.86 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.35), residues: 586 helix: 2.09 (0.30), residues: 285 sheet: -1.53 (0.53), residues: 92 loop : -0.30 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 285 TYR 0.018 0.003 TYR A 36 PHE 0.011 0.002 PHE A 362 TRP 0.011 0.001 TRP A 386 HIS 0.005 0.001 HIS A 667 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 5424) covalent geometry : angle 0.56583 ( 7457) hydrogen bonds : bond 0.03738 ( 261) hydrogen bonds : angle 4.26995 ( 726) metal coordination : bond 0.00227 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.195 Fit side-chains REVERT: A 139 ASP cc_start: 0.8465 (m-30) cc_final: 0.7956 (t0) REVERT: A 264 LYS cc_start: 0.6626 (mptt) cc_final: 0.6078 (ttmt) REVERT: A 271 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7777 (mp) REVERT: A 383 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7693 (tt) REVERT: A 455 ARG cc_start: 0.7463 (ttm170) cc_final: 0.6597 (pmt-80) REVERT: A 626 LYS cc_start: 0.7343 (ttpt) cc_final: 0.6728 (ptpt) outliers start: 14 outliers final: 10 residues processed: 79 average time/residue: 0.0749 time to fit residues: 7.8592 Evaluate side-chains 78 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 633 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 4 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.170576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.143624 restraints weight = 6836.586| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.31 r_work: 0.3629 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5427 Z= 0.111 Angle : 0.526 8.619 7457 Z= 0.252 Chirality : 0.039 0.148 862 Planarity : 0.003 0.028 870 Dihedral : 13.563 83.366 1016 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.52 % Allowed : 18.45 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.35), residues: 586 helix: 2.21 (0.30), residues: 285 sheet: -1.48 (0.52), residues: 94 loop : -0.24 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.015 0.002 TYR A 518 PHE 0.007 0.001 PHE A 309 TRP 0.010 0.001 TRP A 386 HIS 0.005 0.001 HIS A 667 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 5424) covalent geometry : angle 0.52585 ( 7457) hydrogen bonds : bond 0.03391 ( 261) hydrogen bonds : angle 4.14917 ( 726) metal coordination : bond 0.00113 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8449 (m-30) cc_final: 0.7841 (t0) REVERT: A 226 GLN cc_start: 0.7861 (pt0) cc_final: 0.7360 (pm20) REVERT: A 264 LYS cc_start: 0.6619 (mptt) cc_final: 0.6055 (ttmt) REVERT: A 271 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7767 (mp) REVERT: A 383 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7523 (tt) REVERT: A 455 ARG cc_start: 0.7527 (ttm170) cc_final: 0.6557 (pmt-80) REVERT: A 626 LYS cc_start: 0.7246 (ttpt) cc_final: 0.7034 (ptmt) outliers start: 13 outliers final: 10 residues processed: 80 average time/residue: 0.0777 time to fit residues: 8.1841 Evaluate side-chains 73 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 633 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 3 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.169464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.142376 restraints weight = 6740.647| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.32 r_work: 0.3610 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5427 Z= 0.124 Angle : 0.537 9.694 7457 Z= 0.257 Chirality : 0.039 0.161 862 Planarity : 0.003 0.032 870 Dihedral : 13.544 84.676 1016 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.72 % Allowed : 18.25 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.35), residues: 586 helix: 2.15 (0.30), residues: 284 sheet: -1.61 (0.53), residues: 92 loop : -0.14 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 285 TYR 0.013 0.002 TYR A 6 PHE 0.007 0.001 PHE A 362 TRP 0.010 0.001 TRP A 386 HIS 0.006 0.001 HIS A 667 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 5424) covalent geometry : angle 0.53659 ( 7457) hydrogen bonds : bond 0.03477 ( 261) hydrogen bonds : angle 4.15897 ( 726) metal coordination : bond 0.00155 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8468 (m-30) cc_final: 0.7855 (t0) REVERT: A 179 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.7147 (m-30) REVERT: A 226 GLN cc_start: 0.7877 (pt0) cc_final: 0.7358 (pm20) REVERT: A 264 LYS cc_start: 0.6636 (mptt) cc_final: 0.6046 (ttmt) REVERT: A 271 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7764 (mp) REVERT: A 353 MET cc_start: 0.7918 (ttm) cc_final: 0.6947 (mmp) REVERT: A 383 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7497 (tt) REVERT: A 389 GLN cc_start: 0.8063 (mm110) cc_final: 0.7689 (mp10) REVERT: A 626 LYS cc_start: 0.7252 (ttpt) cc_final: 0.7011 (ptmt) outliers start: 14 outliers final: 11 residues processed: 84 average time/residue: 0.0792 time to fit residues: 8.6731 Evaluate side-chains 84 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 633 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 44 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.169554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.142557 restraints weight = 6819.341| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.35 r_work: 0.3616 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5427 Z= 0.122 Angle : 0.537 10.449 7457 Z= 0.257 Chirality : 0.039 0.153 862 Planarity : 0.003 0.029 870 Dihedral : 13.462 84.501 1016 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.11 % Allowed : 18.06 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.35), residues: 586 helix: 2.15 (0.30), residues: 284 sheet: -1.55 (0.54), residues: 92 loop : -0.15 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 285 TYR 0.013 0.002 TYR A 518 PHE 0.007 0.001 PHE A 309 TRP 0.011 0.001 TRP A 386 HIS 0.006 0.001 HIS A 667 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 5424) covalent geometry : angle 0.53750 ( 7457) hydrogen bonds : bond 0.03419 ( 261) hydrogen bonds : angle 4.13123 ( 726) metal coordination : bond 0.00161 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.125 Fit side-chains REVERT: A 139 ASP cc_start: 0.8410 (m-30) cc_final: 0.7799 (t0) REVERT: A 179 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: A 226 GLN cc_start: 0.7809 (pt0) cc_final: 0.7356 (pm20) REVERT: A 264 LYS cc_start: 0.6627 (mptt) cc_final: 0.6124 (ttmt) REVERT: A 271 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7781 (mp) REVERT: A 383 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7427 (tt) REVERT: A 389 GLN cc_start: 0.8068 (mm110) cc_final: 0.7725 (mp10) REVERT: A 626 LYS cc_start: 0.7235 (ttpt) cc_final: 0.7030 (ptmt) outliers start: 16 outliers final: 11 residues processed: 83 average time/residue: 0.0628 time to fit residues: 6.9855 Evaluate side-chains 82 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 633 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.169568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.142404 restraints weight = 6797.460| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.35 r_work: 0.3615 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5427 Z= 0.123 Angle : 0.553 10.667 7457 Z= 0.264 Chirality : 0.039 0.156 862 Planarity : 0.003 0.028 870 Dihedral : 13.393 82.831 1016 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.72 % Allowed : 18.25 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.35), residues: 586 helix: 2.18 (0.29), residues: 284 sheet: -1.66 (0.53), residues: 92 loop : -0.14 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.013 0.002 TYR A 518 PHE 0.008 0.001 PHE A 362 TRP 0.013 0.001 TRP A 75 HIS 0.008 0.001 HIS A 667 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5424) covalent geometry : angle 0.55314 ( 7457) hydrogen bonds : bond 0.03395 ( 261) hydrogen bonds : angle 4.14018 ( 726) metal coordination : bond 0.00148 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.197 Fit side-chains REVERT: A 139 ASP cc_start: 0.8410 (m-30) cc_final: 0.7807 (t0) REVERT: A 179 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.7129 (m-30) REVERT: A 226 GLN cc_start: 0.7809 (pt0) cc_final: 0.7384 (pm20) REVERT: A 264 LYS cc_start: 0.6623 (mptt) cc_final: 0.6117 (ttmt) REVERT: A 271 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7768 (mp) REVERT: A 383 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7447 (tt) REVERT: A 389 GLN cc_start: 0.8069 (mm110) cc_final: 0.7736 (mp10) outliers start: 14 outliers final: 11 residues processed: 83 average time/residue: 0.0628 time to fit residues: 7.1675 Evaluate side-chains 82 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 633 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.168625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.141381 restraints weight = 6801.996| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.35 r_work: 0.3604 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5427 Z= 0.136 Angle : 0.566 10.378 7457 Z= 0.270 Chirality : 0.040 0.160 862 Planarity : 0.003 0.029 870 Dihedral : 13.353 79.200 1016 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.11 % Allowed : 18.06 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.35), residues: 586 helix: 2.11 (0.29), residues: 284 sheet: -1.66 (0.53), residues: 92 loop : -0.19 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 285 TYR 0.013 0.002 TYR A 518 PHE 0.010 0.001 PHE A 664 TRP 0.013 0.001 TRP A 386 HIS 0.009 0.001 HIS A 667 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 5424) covalent geometry : angle 0.56624 ( 7457) hydrogen bonds : bond 0.03545 ( 261) hydrogen bonds : angle 4.16895 ( 726) metal coordination : bond 0.00191 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1238.10 seconds wall clock time: 21 minutes 56.70 seconds (1316.70 seconds total)